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- PDB-5km5: Human Histidine Triad Nucleotide Binding Protein 2 (hHint2) trici... -

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Basic information

Entry
Database: PDB / ID: 5km5
TitleHuman Histidine Triad Nucleotide Binding Protein 2 (hHint2) triciribine 5'-monoposphate catalytic product complex
ComponentsHistidine triad nucleotide-binding protein 2, mitochondrial
KeywordsHYDROLASE / HINT / histidine triad / HIT
Function / homology
Function and homology information


negative regulation of peptidyl-lysine acetylation / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / steroid biosynthetic process / RHOD GTPase cycle / lipid catabolic process / mitochondrial outer membrane / hydrolase activity / nucleotide binding / apoptotic process ...negative regulation of peptidyl-lysine acetylation / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / steroid biosynthetic process / RHOD GTPase cycle / lipid catabolic process / mitochondrial outer membrane / hydrolase activity / nucleotide binding / apoptotic process / mitochondrion / cytoplasm
Similarity search - Function
Histidine triad (HIT) protein / HIT domain / Histidine triad, conserved site / HIT domain signature. / HIT domain profile. / HIT-like domain / HIT-like / HIT family, subunit A / HIT-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-TR5 / Adenosine 5'-monophosphoramidase HINT2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMaize, K.M. / Finzel, B.C.
CitationJournal: Mol. Pharm. / Year: 2017
Title: A Crystal Structure Based Guide to the Design of Human Histidine Triad Nucleotide Binding Protein 1 (hHint1) Activated ProTides.
Authors: Maize, K.M. / Shah, R. / Strom, A. / Kumarapperuma, S. / Zhou, A. / Wagner, C.R. / Finzel, B.C.
History
DepositionJun 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Database references / Category: citation_author
Revision 1.2Oct 18, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Nov 15, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histidine triad nucleotide-binding protein 2, mitochondrial
B: Histidine triad nucleotide-binding protein 2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0735
Polymers30,4432
Non-polymers6303
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-25 kcal/mol
Surface area9370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.129, 76.045, 77.821
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Histidine triad nucleotide-binding protein 2, mitochondrial / HINT-2 / HINT-3 / HIT-17kDa


Mass: 15221.329 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HINT2 / Plasmid: pMCSG9 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 pLysS / References: UniProt: Q9BX68, Hydrolases
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-TR5 / 5-methyl-1-(5-O-phosphono-beta-D-ribofuranosyl)-1,5-dihydro-1,4,5,6,8-pentaazaacenaphthylen-3-amine / Triciribine phosphate


Mass: 400.284 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H17N6O7P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.85 Å3/Da / Density % sol: 33.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 100 mM MES, 45% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→76.045 Å / Num. obs: 13736 / % possible obs: 99.7 % / Redundancy: 6 % / Biso Wilson estimate: 26.16 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 15.9
Reflection shell

Diffraction-ID: 1 / Rejects: _ / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique all
2.1-2.1075.80.287858147
9.741-76.0455.10.035888174

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.15data extraction
PHENIXrefinement
REFMACrefinement
PHASERphasing
SCALAdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4INC

4inc


Resolution: 2.1→38.023 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2242 667 4.87 %
Rwork0.1713 13021 -
obs0.1739 13688 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 60.41 Å2 / Biso mean: 27.3952 Å2 / Biso min: 15.17 Å2
Refinement stepCycle: final / Resolution: 2.1→38.023 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1662 0 41 64 1767
Biso mean--31.08 32.32 -
Num. residues----213
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081744
X-RAY DIFFRACTIONf_angle_d1.3282374
X-RAY DIFFRACTIONf_chiral_restr0.053263
X-RAY DIFFRACTIONf_plane_restr0.006306
X-RAY DIFFRACTIONf_dihedral_angle_d14.931658
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.26210.26831320.21262534266699
2.2621-2.48980.28551320.19942549268199
2.4898-2.84990.23791210.22584270599
2.8499-3.59020.23221430.17942598274199
3.5902-38.02870.1851390.13927562895100

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